Title: Visualisations for Generalized Additive Models
Description: Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models that exploit the additive structure of such models, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.
Author: Matteo Fasiolo [aut, cre],
Raphael Nedellec [aut],
Yannig Goude [ctb],
Christian Capezza [ctb],
Simon N. Wood [ctb]
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between mgcViz versions 0.1.6 dated 2020-03-04 and 0.1.8 dated 2021-08-21
DESCRIPTION | 14 MD5 | 109 R/I_compute_qq_gam.R | 2 R/I_initialize.R | 2 R/I_multinomJacobian.R | 1 R/I_prepareInnerSI.R |only R/I_prepareNested.R |only R/L_ciBar.R | 3 R/L_ciLine.R | 2 R/L_fitBar.R | 3 R/L_fitLine.R | 2 R/L_fitPoints.R | 3 R/L_gridCheck1D.R | 33 R/L_rug.R | 3 R/check_gamViz.R | 4 R/gamm4V.R | 2 R/gammV.R | 2 R/getViz.R | 4 R/plotSlice.R | 2 R/plot_mgcv_smooth_1D.R | 9 R/plot_multi_mgcv_smooth_1D.R | 9 R/plot_si_smooth_1D.R |only R/postSim.R | 21 R/print_plotGam.R | 2 R/simulate_gam.R | 10 R/sm.R | 4 build/vignette.rds |binary inst/CITATION | 2 inst/doc/mgcviz.R | 93 inst/doc/mgcviz.html |12421 ++++++++++++++++++++++++++--------------- inst/doc/mgcviz.rmd | 7 man/gammV.Rd | 4 man/getGam.Rd | 2 man/l_fitRaster.Rd | 2 man/l_gridCheck2D.Rd | 2 man/l_gridQCheck2D.Rd | 2 man/l_vline.Rd | 2 man/plot.mgcv.smooth.1D.Rd | 9 man/plot.mgcv.smooth.2D.Rd | 2 man/plot.mgcv.smooth.MD.Rd | 2 man/plot.mrf.smooth.Rd | 2 man/plot.ptermFactor.Rd | 2 man/plot.ptermInteraction.Rd | 2 man/plot.ptermNumeric.Rd | 2 man/plot.random.effect.Rd | 2 man/plot.sos.smooth.Rd | 2 man/plotDiff.mgcv.smooth.1D.Rd | 2 man/plotDiff.mgcv.smooth.2D.Rd | 2 man/plotDiff.sos.smooth.Rd | 2 man/plotRGL.mgcv.smooth.2D.Rd | 2 man/plotRGL.mgcv.smooth.MD.Rd | 2 man/plotSlice.Rd | 2 man/postSim.Rd | 6 man/print.checkGam.Rd | 2 man/print.plotGam.Rd | 2 man/simulate.gam.Rd | 6 vignettes/mgcviz.rmd | 7 57 files changed, 8218 insertions(+), 4625 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.6.3 dated 2021-07-23 and 2.6.5 dated 2021-08-21
DESCRIPTION | 6 - MD5 | 69 ++++++++------- NEWS.md | 14 +++ R/ISSR800.R | 4 R/SDA_coecoclass.R |only R/SDA_properties.R | 18 +--- R/SDA_query.R | 22 ++--- R/WCS-utils.R | 4 R/createStaticNASIS.R | 15 ++- R/fetchNASIS.R | 6 - R/fetchNASIS_pedons.R | 56 ++++++++---- R/fetchOSD.R | 2 R/fetchRaCA.R | 26 +++-- R/fetchSoilGrids.R | 152 ++++++++++++++++++++++++++++------- R/get_hz_data_from_NASIS_db.R | 11 +- R/mukey-WCS.R | 4 R/seriesExtent.R | 4 R/siblings.R | 67 +++++++-------- R/taxaExtent.R | 4 build/partial.rdb |binary man/ISSR800.wcs.Rd | 2 man/createStaticNASIS.Rd | 2 man/fetchNASIS.Rd | 3 man/fetchOSD.Rd | 2 man/fetchRaCA.Rd | 8 + man/fetchSoilGrids.Rd | 43 ++++++++- man/get_SDA_coecoclass.Rd |only man/get_SDA_property.Rd | 9 -- man/get_hz_data_from_NASIS_db.Rd | 3 man/mukey.wcs.Rd | 2 man/seriesExtent.Rd | 2 man/siblings.Rd | 45 ++++------ man/taxaExtent.Rd | 2 tests/testthat/test-SDA_coecoclass.R |only tests/testthat/test-fetchNASIS.R | 8 + tests/testthat/test-fetchSoilGrids.R | 17 +++ tests/testthat/test-siblings.R | 21 ++++ 37 files changed, 439 insertions(+), 214 deletions(-)
Title: 'SQLite' Interface for R
Description: Embeds the 'SQLite' database engine in R and
provides an interface compliant with the 'DBI' package. The source for
the 'SQLite' engine is included.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
SQLite Authors [ctb] (for the included SQLite sources),
Liam Healy [ctb] (for the included SQLite sources),
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RSQLite versions 2.2.7 dated 2021-04-22 and 2.2.8 dated 2021-08-21
DESCRIPTION | 10 MD5 | 31 NEWS.md | 8 R/table.R | 2 R/utils.R | 4 R/zzz.R | 4 build/vignette.rds |binary inst/doc/RSQLite.html | 1 src/DbConnection.cpp | 48 src/RcppExports.cpp | 5 src/vendor/boost/detail/fenv.hpp |only src/vendor/sqlite3/regexp.c | 37 src/vendor/sqlite3/sqlite3.c | 7172 +++++++++++++++++++++--------------- src/vendor/sqlite3/sqlite3.h | 133 tests/testthat/helper-DBItest.R | 2 tests/testthat/test-dbConnect.R | 2 tests/testthat/test-extendedTypes.R | 12 17 files changed, 4440 insertions(+), 3031 deletions(-)
Title: Iterative Solvers for (Sparse) Linear System of Equations
Description: Solving a system of linear equations is one of the most fundamental
computational problems for many fields of mathematical studies, such as
regression problems from statistics or numerical partial differential equations.
We provide basic stationary iterative solvers such as Jacobi, Gauss-Seidel,
Successive Over-Relaxation and SSOR methods. Nonstationary, also known as
Krylov subspace methods are also provided. Sparse matrix computation is also supported
in that solving large and sparse linear systems can be manageable using 'Matrix' package
along with 'RcppArmadillo'. For a more detailed description, see a book by Saad (2003)
<doi:10.1137/1.9780898718003>.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kisungyou@outlook.com>
Diff between Rlinsolve versions 0.3.1 dated 2020-05-05 and 0.3.2 dated 2021-08-21
DESCRIPTION | 15 ++++++-------- LICENSE |only MD5 | 25 ++++++++++++----------- NAMESPACE | 1 NEWS.md | 4 +++ R/init.R | 2 - R/lsolve_GS.R | 2 - R/lsolve_JACOBI.R | 2 - R/lsolve_SOR.R | 2 - R/lsolve_SSOR.R | 2 - R/package-Rlinsolve.R | 1 build/partial.rdb |binary inst/REFERENCES.bib | 53 ++++++++------------------------------------------ src/RcppExports.cpp | 5 ++++ 14 files changed, 45 insertions(+), 69 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Eddelbuettel [ctb],
The authors of Shiny [cph],
The authors of knitr [cph],
Jeroen Ooms [ctb],
Yohann Demont [ctb],
Joshua Ulrich [ctb],
Xavier Fernandez i Marin [ctb],
George Helffrich [ctb],
Ivan Krylov [ctb],
Michael Sumner [ctb]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 0.107.10 dated 2021-07-22 and 0.107.14 dated 2021-08-21
rgl-0.107.10/rgl/inst/htmlwidgets/lib/rglClass/rglClass.min.js |only rgl-0.107.14/rgl/DESCRIPTION | 6 rgl-0.107.14/rgl/MD5 | 37 - rgl-0.107.14/rgl/NAMESPACE | 1 rgl-0.107.14/rgl/NEWS.md | 11 rgl-0.107.14/rgl/R/rglwidget.R | 14 rgl-0.107.14/rgl/configure | 4 rgl-0.107.14/rgl/configure.ac | 4 rgl-0.107.14/rgl/demo/shinyMouse.R | 3 rgl-0.107.14/rgl/inst/doc/WebGL.R | 10 rgl-0.107.14/rgl/inst/doc/WebGL.Rmd | 10 rgl-0.107.14/rgl/inst/doc/WebGL.html | 84 +- rgl-0.107.14/rgl/inst/doc/pkgdown.R | 6 rgl-0.107.14/rgl/inst/doc/pkgdown.Rmd | 7 rgl-0.107.14/rgl/inst/doc/pkgdown.html | 9 rgl-0.107.14/rgl/inst/doc/rgl.html | 320 +++++----- rgl-0.107.14/rgl/man/asRow.Rd | 4 rgl-0.107.14/rgl/man/rglShared.Rd | 3 rgl-0.107.14/rgl/vignettes/WebGL.Rmd | 10 rgl-0.107.14/rgl/vignettes/pkgdown.Rmd | 7 20 files changed, 301 insertions(+), 249 deletions(-)
Title: Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix
linear algebra as used in multivariate statistical methods. These functions are
mainly for tutorial purposes in learning matrix algebra ideas using R. In some
cases, functions are provided for concepts available elsewhere in R, but where
the function call or name is not obvious. In other cases, functions are provided
to show or demonstrate an algorithm. In addition, a collection of functions are
provided for drawing vector diagrams in 2D and 3D.
Author: Michael Friendly [aut, cre] (<https://orcid.org/0000-0002-3237-0941>),
John Fox [aut],
Phil Chalmers [aut],
Georges Monette [ctb],
Gaston Sanchez [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between matlib versions 0.9.4 dated 2020-10-29 and 0.9.5 dated 2021-08-21
DESCRIPTION | 11 MD5 | 30 NEWS.md | 5 R/proj.R | 7 build/vignette.rds |binary inst/doc/data-beta.html | 4826 +---------------------------------------- inst/doc/det-ex1.html | 384 --- inst/doc/det-ex2.html | 338 -- inst/doc/eigen-ex1.html | 312 -- inst/doc/eigen-ex2.html | 326 -- inst/doc/ginv.html | 308 -- inst/doc/gramreg.html | 354 --- inst/doc/inv-ex1.html | 398 --- inst/doc/inv-ex2.html | 336 -- inst/doc/linear-equations.html | 405 --- man/Proj.Rd | 7 16 files changed, 821 insertions(+), 7226 deletions(-)
Title: Send Email Messages
Description: A light, simple tool for sending emails with minimal dependencies.
Author: Andrew B. Collier [aut, cre],
Matt Dennis [ctb],
Antoine Bichat [ctb] (<https://orcid.org/0000-0001-6599-7081>),
Daniel Fahey [ctb],
Johann R. Kleinbub [ctb],
Panagiotis Moulos [ctb]
Maintainer: Andrew B. Collier <andrew.b.collier@gmail.com>
Diff between emayili versions 0.4.15 dated 2021-07-30 and 0.4.16 dated 2021-08-21
DESCRIPTION | 10 - MD5 | 54 +++-- NAMESPACE | 27 ++ R/address.R | 347 +++++++++++++++++++++++++++--------- R/emayili.R | 7 R/parties.R |only R/server.R | 18 + R/utils.R |only man/address.Rd |only man/as.address.Rd |only man/as.character.envelope.Rd | 16 - man/as.character.vctrs_address.Rd |only man/bcc.Rd | 2 man/cc.Rd | 2 man/compare.Rd |only man/compliant.Rd |only man/display.Rd |only man/domain.Rd |only man/format.vctrs_address.Rd |only man/from.Rd | 2 man/local.Rd |only man/new_address.Rd |only man/parameter_value_encode.Rd | 8 man/parties.Rd |only man/pipe.Rd |only man/print.vctrs_address.Rd |only man/raw.Rd |only man/reply.Rd | 2 man/sender.Rd | 2 man/server.Rd | 6 man/to.Rd | 2 man/vec_ptype_abbr.vctrs_address.Rd |only man/vec_ptype_full.vctrs_address.Rd |only tests/testthat/test-address-parts.R |only tests/testthat/test-address.R | 109 +++++------ tests/testthat/test-compliant.R |only tests/testthat/test-display.R |only tests/testthat/test-envelope.R | 10 - tests/testthat/test-sanitise.R |only 39 files changed, 431 insertions(+), 193 deletions(-)
Title: Functions and C++ Header Files for Computation on Manifolds
Description: We provide a number of algorithms to estimate fundamental statistics including Fréchet mean and geometric median for manifold-valued data. Also, C++ header files are contained that implement elementary operations on manifolds such as Sphere, Grassmann, and others. See Bhattacharya and Bhattacharya (2012) <doi:10.1017/CBO9781139094764> if you are interested in statistics on manifolds, and Absil et al (2007, ISBN:9780691132983) on computational aspects of optimization on matrix manifolds.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kisungyou@outlook.com>
Diff between RiemBase versions 0.2.4 dated 2020-03-21 and 0.2.5 dated 2021-08-21
DESCRIPTION | 19 +++++++++---------- LICENSE |only MD5 | 19 ++++++++++--------- NEWS.md | 39 +++++++++++++++++++++++---------------- R/init.R | 2 +- R/rbase.pdist.R | 2 ++ README.md | 19 +++++++++++++------ build/partial.rdb |binary inst/REFERENCES.bib | 5 ----- man/rbase.pdist.Rd | 2 ++ src/RcppExports.cpp | 5 +++++ 11 files changed, 65 insertions(+), 47 deletions(-)
Title: Distance Measures for Networks
Description: Network is a prevalent form of data structure in many fields. As an object of analysis, many distance or metric measures have been proposed to define the concept of similarity between two networks. We provide a number of distance measures for networks. See Jurman et al (2011) <doi:10.3233/978-1-60750-692-8-227> for an overview on spectral class of inter-graph distance measures.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kisungyou@outlook.com>
Diff between NetworkDistance versions 0.3.3 dated 2020-05-08 and 0.3.4 dated 2021-08-21
DESCRIPTION | 13 ++---- MD5 | 18 ++++---- NEWS.md | 4 + R/zzz.R | 2 README.md | 111 +++++++++++++++------------------------------------- build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 23 +--------- inst/doc/basics.pdf |binary src/RcppExports.cpp | 5 ++ 10 files changed, 63 insertions(+), 113 deletions(-)
More information about NetworkDistance at CRAN
Permanent link
Title: Matrix Completion, Imputation, and Inpainting Methods
Description: Filling in the missing entries of a partially observed data is one of fundamental problems in various disciplines of mathematical science. For many cases, data at our interests have canonical form of matrix in that the problem is posed upon a matrix with missing values to fill in the entries under preset assumptions and models. We provide a collection of methods from multiple disciplines under Matrix Completion, Imputation, and Inpainting. See Davenport and Romberg (2016) <doi:10.1109/JSTSP.2016.2539100> for an overview of the topic.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kisungyou@outlook.com>
Diff between filling versions 0.2.2 dated 2020-07-02 and 0.2.3 dated 2021-08-21
DESCRIPTION | 12 ++++----- MD5 | 24 +++++++++--------- NEWS.md | 4 +++ R/lena128.R | 4 --- R/lena256.R | 4 --- R/lena64.R | 4 --- R/zzz.R | 2 - build/partial.rdb |binary inst/REFERENCES.bib | 66 +++++++++------------------------------------------- man/lena128.Rd | 3 -- man/lena256.Rd | 3 -- man/lena64.Rd | 3 -- src/RcppExports.cpp | 5 +++ 13 files changed, 46 insertions(+), 88 deletions(-)
Title: Declare and Diagnose Research Designs
Description: Researchers can characterize and learn about the properties of
research designs before implementation using `DeclareDesign`. Ex ante
declaration and diagnosis of designs can help researchers clarify the
strengths and limitations of their designs and to improve their
properties, and can help readers evaluate a research strategy prior
to implementation and without access to results. It can also make it
easier for designs to be shared, replicated, and critiqued.
Author: Graeme Blair [aut, cre] (<https://orcid.org/0000-0001-9164-2102>),
Jasper Cooper [aut] (<https://orcid.org/0000-0002-8639-3188>),
Alexander Coppock [aut] (<https://orcid.org/0000-0002-5733-2386>),
Macartan Humphreys [aut] (<https://orcid.org/0000-0001-7029-2326>),
Neal Fultz [aut]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between DeclareDesign versions 0.26.0 dated 2021-02-14 and 0.28.0 dated 2021-08-21
DESCRIPTION | 9 MD5 | 182 ++++++++--------- NAMESPACE | 2 NEWS.md | 5 R/compare_designs.R | 14 - R/compare_diagnoses.R | 58 ++--- R/construct_design.R | 4 R/declare_assignment.R | 21 + R/declare_diagnosands.R | 12 - R/declare_estimator.R | 18 - R/declare_inquiry.R | 10 R/declare_measurement.R | 2 R/declare_reveal.R | 8 R/declare_sampling.R | 10 R/declare_test.R | 6 R/design_helper_functions.R | 16 - R/design_print_summary.R | 4 R/diagnose_design.R | 22 +- R/diagnosis_helper_functions.R | 10 R/draw_functions.R | 26 -- R/expand_design.R | 2 R/get_functions.R | 12 - R/modify_design.R | 4 R/set_citation.R | 2 R/set_diagnosands.R | 2 R/simulate_design.R | 16 - man/compare_diagnoses.Rd | 8 man/compare_functions.Rd | 8 man/declare_assignment.Rd | 14 - man/declare_design.Rd | 4 man/declare_diagnosands.Rd | 6 man/declare_estimator.Rd | 6 man/declare_inquiry.Rd | 6 man/declare_measurement.Rd | 2 man/declare_reveal.Rd | 8 man/declare_sampling.Rd | 4 man/declare_test.Rd | 4 man/diagnose_design.Rd | 4 man/diagnosis_helpers.Rd | 2 man/draw_functions.Rd | 16 - man/expand_design.Rd | 2 man/get_functions.Rd | 4 man/modify_design.Rd | 4 man/post_design.Rd | 12 - man/run_design.Rd | 2 man/set_citation.Rd | 2 man/set_diagnosands.Rd | 2 man/simulate_design.Rd | 2 tests/testthat/test-alternative-df-compatibility.R | 2 tests/testthat/test-assignment.R | 77 +++---- tests/testthat/test-attrition.R | 2 tests/testthat/test-bootstrap-diagnosands.R | 10 tests/testthat/test-citation.R | 2 tests/testthat/test-compare-designs.R | 14 - tests/testthat/test-compare-diagnoses.R | 33 ++- tests/testthat/test-continuous-pos.R | 4 tests/testthat/test-declare-design.R | 10 tests/testthat/test-declare-step.R | 2 tests/testthat/test-demo.R | 12 - tests/testthat/test-design-library.R | 2 tests/testthat/test-design-summary.R | 4 tests/testthat/test-diagnosands.R | 34 +-- tests/testthat/test-diagnose-design.R | 36 +-- tests/testthat/test-environment-issues.R | 2 tests/testthat/test-estimands.R | 32 +- tests/testthat/test-estimators.R | 28 +- tests/testthat/test-expand-design.R | 6 tests/testthat/test-factorial.R | 4 tests/testthat/test-fanout.R | 8 tests/testthat/test-get-estimates.R | 28 +- tests/testthat/test-get-star.R | 4 tests/testthat/test-labels.R | 4 tests/testthat/test-model-summary.R | 30 +- tests/testthat/test-model.R | 4 tests/testthat/test-modify-design.R | 10 tests/testthat/test-multiple-estimands-one-estimator.R | 6 tests/testthat/test-multiple-estimators.R | 2 tests/testthat/test-multiple-pos.R | 2 tests/testthat/test-name-steps.R | 4 tests/testthat/test-names-and-labels.R | 12 - tests/testthat/test-noncompliance.R | 8 tests/testthat/test-paper.R | 4 tests/testthat/test-plus.R | 6 tests/testthat/test-print-code.R | 8 tests/testthat/test-quick-design.R | 6 tests/testthat/test-reshape-diagnosis.R | 26 +- tests/testthat/test-reveal-outcomes.R | 14 - tests/testthat/test-sampling.R | 74 ++---- tests/testthat/test-simulate-design.R | 16 - tests/testthat/test-subset.R | 6 tests/testthat/test-sugar.R | 6 tests/testthat/test-test.R | 2 92 files changed, 600 insertions(+), 605 deletions(-)
Title: Customise the Appearance of 'shinydashboard' Applications using
Themes
Description: Allows manual creation of themes and logos to be used in
applications created using the 'shinydashboard' package. Removes the need to
change the underlying css code by wrapping it into a set of convenient R
functions.
Author: Nik Lilovski [aut, cre]
Maintainer: Nik Lilovski <nik.lilovski@outlook.com>
Diff between dashboardthemes versions 1.1.3 dated 2020-08-26 and 1.1.5 dated 2021-08-21
DESCRIPTION | 7 MD5 | 16 NEWS.md | 6 R/CreateTheme_shinyDashboardThemeDIY.R | 12 README.md | 2 build/vignette.rds |binary inst/doc/using_dashboardthemes.html | 646 +++------- man/shinyDashboardThemeDIY.Rd | 8 tests/testthat/test-assets/CreateTheme_shinyDashboardThemeDIY/ExpectedOutput.css | 2 9 files changed, 263 insertions(+), 436 deletions(-)
More information about dashboardthemes at CRAN
Permanent link
Title: Analysis of Diversity
Description: Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Author: Sandrine Pavoine
Maintainer: Sandrine Pavoine <sandrine.pavoine@mnhn.fr>
Diff between adiv versions 2.0.1 dated 2020-08-26 and 2.1 dated 2021-08-21
DESCRIPTION | 13 ++-- MD5 | 51 ++++++++++------ NAMESPACE | 6 + R/DJac.R | 89 +++++++++++++++++------------ R/FPdivparam.R |only R/betaUniqueness.R |only R/dbMANOVAspecies.R |only R/dbMANOVAspecies_pairwise.R |only R/dislptransport.R |only R/distinctAb.R |only R/distinctDis.R | 63 +++++++++++++++----- R/distinctTree.R | 107 ++++++++++++++++++++++++----------- R/plot.FPdivparam.R |only R/summary.dbMANOVAspecies_pairwise.R |only build/partial.rdb |binary data/batcomm.rda |binary inst/CITATION | 3 inst/doc/adivGuide.pdf |binary man/FPdivparam.Rd |only man/batcomm.Rd | 30 ++++++++- man/betaTreeUniqueness.Rd | 2 man/betaUniqueness.Rd |only man/dbMANOVAspecies.Rd |only man/dislptransport.Rd |only man/distinctAb.Rd |only man/distinctDis.Rd | 23 +++++-- man/distinctTree.Rd | 20 ++++-- man/divparam.Rd | 2 man/eveparam.Rd | 2 man/evodivparam.Rd | 4 - man/evoeveparam.Rd | 2 man/evouniparam.Rd | 4 - vignettes/adivGuide.Rnw | 28 +++++++-- 33 files changed, 307 insertions(+), 142 deletions(-)
Title: Estimate the Shattering Coefficient for a Particular Dataset
Description: The Statistical Learning Theory (SLT) provides the theoretical background to ensure that a supervised algorithm generalizes the mapping f:X -> Y given f is selected from its search space bias F. This formal result depends on the Shattering coefficient function N(F,2n) to upper bound the empirical risk minimization principle, from which one can estimate the necessary training sample size to ensure the probabilistic learning convergence and, most importantly, the characterization of the capacity of F, including its under and overfitting abilities while addressing specific target problems. In this context, we propose a new approach to estimate the maximal number of hyperplanes required to shatter a given sample, i.e., to separate every pair of points from one another, based on the recent contributions by Har-Peled and Jones in the dataset partitioning scenario, and use such foundation to analytically compute the Shattering coefficient function for both binary and multi-class problems. As main contributions, one can use our approach to study the complexity of the search space bias F, estimate training sample sizes, and parametrize the number of hyperplanes a learning algorithm needs to address some supervised task, what is specially appealing to deep neural networks. Reference: de Mello, R.F. (2019) "On the Shattering Coefficient of Supervised Learning Algorithms" <arXiv:1911.05461>; de Mello, R.F., Ponti, M.A. (2018, ISBN: 978-3319949888) "Machine Learning: A Practical Approach on the Statistical Learning Theory".
Author: Rodrigo F. de Mello [aut, cre]
(<https://orcid.org/0000-0002-0435-3992>)
Maintainer: Rodrigo F. de Mello <mellorf@gmail.com>
Diff between shattering versions 1.0.6 dated 2021-06-02 and 1.0.7 dated 2021-08-21
DESCRIPTION | 6 ++-- MD5 | 11 +++++--- NAMESPACE | 2 + R/apply_classifier.R | 13 ++++++++++ R/complexity_analysis.R | 62 +++++++++++++++++++++++++++--------------------- R/number_regions.R |only man/apply_classifier.Rd |only man/number_regions.Rd |only 8 files changed, 60 insertions(+), 34 deletions(-)
Title: 'Rcpp' Bindings for the 'fast_float' Header-Only Library for
Number Parsing
Description: Converting ascii text into (floating-point) numeric values is a
very common problem. The 'fast_float' header-only C++ library by Daniel Lemire
does it very well and very fast at up to or over to 1 gigabyte per second as
described in more detail in <arXiv:2101.11408>. 'fast_float' is licensed under
the Apache 2.0 license and provided here for use by other R packages via a simple
'LinkingTo:' statement.
Author: Dirk Eddelbuettel, Brendan Knapp
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppFastFloat versions 0.0.2 dated 2021-02-13 and 0.0.3 dated 2021-08-21
ChangeLog | 16 ++++++++++++++++ DESCRIPTION | 11 ++++++----- MD5 | 10 +++++----- inst/NEWS.Rd | 7 +++++++ inst/include/fast_float/float_common.h | 2 +- src/Makevars | 2 ++ 6 files changed, 37 insertions(+), 11 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. pathfindR is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
pathfindR also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in pathfindR are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for
Comprehensive Identification of Enriched Pathways in Omics Data Through
Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.
Author: Ege Ulgen [cre, cph] (<https://orcid.org/0000-0003-2090-3621>),
Ozan Ozisik [aut] (<https://orcid.org/0000-0001-5980-8002>)
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 1.6.1 dated 2021-01-04 and 1.6.2 dated 2021-08-21
pathfindR-1.6.1/pathfindR/man/run_pathfindr.Rd |only pathfindR-1.6.2/pathfindR/DESCRIPTION | 7 pathfindR-1.6.2/pathfindR/MD5 | 40 pathfindR-1.6.2/pathfindR/NEWS.md | 21 pathfindR-1.6.2/pathfindR/R/comparison_functions.R | 6 pathfindR-1.6.2/pathfindR/R/data_generation.R | 29 pathfindR-1.6.2/pathfindR/R/scoring.R | 10 pathfindR-1.6.2/pathfindR/R/visualization_functions.R | 29 pathfindR-1.6.2/pathfindR/build/vignette.rds |binary pathfindR-1.6.2/pathfindR/inst/doc/comparing_results.html | 294 --- pathfindR-1.6.2/pathfindR/inst/doc/intro_vignette.html | 932 ++++------ pathfindR-1.6.2/pathfindR/inst/doc/manual_execution.html | 378 ---- pathfindR-1.6.2/pathfindR/inst/doc/non_hs_analysis.html | 578 ++---- pathfindR-1.6.2/pathfindR/inst/doc/obtain_data.html | 336 --- pathfindR-1.6.2/pathfindR/inst/doc/visualization_vignette.html | 324 --- pathfindR-1.6.2/pathfindR/man/UpSet_plot.Rd | 2 pathfindR-1.6.2/pathfindR/man/get_biogrid_pin.Rd | 4 pathfindR-1.6.2/pathfindR/man/run_pathfindR.Rd |only pathfindR-1.6.2/pathfindR/tests/testthat/test-comparison_functions.R | 9 pathfindR-1.6.2/pathfindR/tests/testthat/test-data_generation.R | 2 pathfindR-1.6.2/pathfindR/tests/testthat/test-scoring.R | 12 pathfindR-1.6.2/pathfindR/tests/testthat/test-visualization_functions.R | 4 22 files changed, 906 insertions(+), 2111 deletions(-)
Title: Spatial Analysis of Vectra Immunoflourescent Data
Description: Visualization and analysis of Vectra Immunoflourescent
data. Options for calculating both the univariate and bivariate Ripley's K
are included. Calculations are performed using a permutation-based
approach presented by Wilson et al. <doi:10.1101/2021.04.27.21256104>.
Author: Jordan Creed [aut],
Ram Thapa [aut],
Christopher Wilson [aut],
Alex Soupir [aut],
Brooke Fridley [cph],
Fridley Lab [cre]
Maintainer: Fridley Lab <fridley.lab@moffitt.org>
Diff between spatialTIME versions 1.0.0 dated 2021-05-14 and 1.1.0 dated 2021-08-21
spatialTIME-1.0.0/spatialTIME/tests |only spatialTIME-1.1.0/spatialTIME/DESCRIPTION | 26 spatialTIME-1.1.0/spatialTIME/MD5 | 46 spatialTIME-1.1.0/spatialTIME/NAMESPACE | 5 spatialTIME-1.1.0/spatialTIME/R/create_mif.R | 28 spatialTIME-1.1.0/spatialTIME/R/data-example-spatial.R | 2 spatialTIME-1.1.0/spatialTIME/R/global.R |only spatialTIME-1.1.0/spatialTIME/R/plot_immunoflo.R | 71 - spatialTIME-1.1.0/spatialTIME/R/print.R | 4 spatialTIME-1.1.0/spatialTIME/R/ripleys_k.R | 528 +++++------ spatialTIME-1.1.0/spatialTIME/R/subset_mif.R |only spatialTIME-1.1.0/spatialTIME/R/utils-helpers.R | 807 +++++++++++------ spatialTIME-1.1.0/spatialTIME/R/utils-pipe.R | 3 spatialTIME-1.1.0/spatialTIME/inst/doc/intro.R | 253 ++--- spatialTIME-1.1.0/spatialTIME/inst/doc/intro.Rmd | 366 +++---- spatialTIME-1.1.0/spatialTIME/inst/doc/intro.html | 354 ++++--- spatialTIME-1.1.0/spatialTIME/man/NN_G.Rd |only spatialTIME-1.1.0/spatialTIME/man/bi_NN_G.Rd |only spatialTIME-1.1.0/spatialTIME/man/bi_ripleys_k.Rd | 55 - spatialTIME-1.1.0/spatialTIME/man/create_mif.Rd | 10 spatialTIME-1.1.0/spatialTIME/man/example_spatial.Rd | 2 spatialTIME-1.1.0/spatialTIME/man/pipe.Rd | 5 spatialTIME-1.1.0/spatialTIME/man/plot_immunoflo.Rd | 10 spatialTIME-1.1.0/spatialTIME/man/ripleys_k.Rd | 50 - spatialTIME-1.1.0/spatialTIME/man/subset_mif.Rd |only spatialTIME-1.1.0/spatialTIME/vignettes/intro.Rmd | 366 +++---- 26 files changed, 1591 insertions(+), 1400 deletions(-)
Title: Forecast Modelling for Online Applications
Description: A framework for fitting adaptive forecasting models. Provides a way to use forecasts as input to models, e.g. weather forecasts for energy related forecasting. The models can be fitted recursively and can easily be setup for updating parameters when new data arrives. See the included vignettes, the website <https://onlineforecasting.org> and the paper "Short-term heat load forecasting for single family houses" <doi:10.1016/j.enbuild.2013.04.022>.
Author: Peder Bacher [cre],
Hjorleifur G Bergsteinsson [aut]
Maintainer: Peder Bacher <pbac@dtu.dk>
Diff between onlineforecast versions 0.9.3 dated 2020-09-15 and 0.10.0 dated 2021-08-21
onlineforecast-0.10.0/onlineforecast/DESCRIPTION | 9 onlineforecast-0.10.0/onlineforecast/MD5 | 134 - onlineforecast-0.10.0/onlineforecast/NAMESPACE | 10 onlineforecast-0.10.0/onlineforecast/R/as.data.list.R | 7 onlineforecast-0.10.0/onlineforecast/R/bspline.R | 7 onlineforecast-0.10.0/onlineforecast/R/cache_name.R | 24 onlineforecast-0.10.0/onlineforecast/R/complete_cases.R |only onlineforecast-0.10.0/onlineforecast/R/data.list.R | 119 - onlineforecast-0.10.0/onlineforecast/R/depth.R |only onlineforecast-0.10.0/onlineforecast/R/flattenlist.R |only onlineforecast-0.10.0/onlineforecast/R/forecastmodel.R | 95 onlineforecast-0.10.0/onlineforecast/R/forecastmodel.R-documentation.R | 4 onlineforecast-0.10.0/onlineforecast/R/in_range.R | 27 onlineforecast-0.10.0/onlineforecast/R/lagdf.R | 8 onlineforecast-0.10.0/onlineforecast/R/lagdl.R |only onlineforecast-0.10.0/onlineforecast/R/lapply.R | 20 onlineforecast-0.10.0/onlineforecast/R/lm_fit.R | 13 onlineforecast-0.10.0/onlineforecast/R/lm_optim.R | 40 onlineforecast-0.10.0/onlineforecast/R/make_input.R | 2 onlineforecast-0.10.0/onlineforecast/R/make_periodic.R |only onlineforecast-0.10.0/onlineforecast/R/make_tday.R | 30 onlineforecast-0.10.0/onlineforecast/R/operator_multiply.R | 62 onlineforecast-0.10.0/onlineforecast/R/plot_ts.R | 40 onlineforecast-0.10.0/onlineforecast/R/plotly_ts.R | 10 onlineforecast-0.10.0/onlineforecast/R/residuals.R | 24 onlineforecast-0.10.0/onlineforecast/R/rls_fit.R | 6 onlineforecast-0.10.0/onlineforecast/R/rls_optim.R | 46 onlineforecast-0.10.0/onlineforecast/R/rls_summary.R | 24 onlineforecast-0.10.0/onlineforecast/R/rmse.R | 2 onlineforecast-0.10.0/onlineforecast/R/score.R | 87 onlineforecast-0.10.0/onlineforecast/R/step_optim.R |only onlineforecast-0.10.0/onlineforecast/build/vignette.rds |binary onlineforecast-0.10.0/onlineforecast/inst/CITATION | 10 onlineforecast-0.10.0/onlineforecast/inst/doc/forecast-evaluation.R | 19 onlineforecast-0.10.0/onlineforecast/inst/doc/forecast-evaluation.Rmd | 217 +- onlineforecast-0.10.0/onlineforecast/inst/doc/forecast-evaluation.html | 579 +++-- onlineforecast-0.10.0/onlineforecast/inst/doc/model-selection.R |only onlineforecast-0.10.0/onlineforecast/inst/doc/model-selection.Rmd |only onlineforecast-0.10.0/onlineforecast/inst/doc/model-selection.html |only onlineforecast-0.10.0/onlineforecast/inst/doc/setup-and-use-model.R | 10 onlineforecast-0.10.0/onlineforecast/inst/doc/setup-and-use-model.Rmd | 62 onlineforecast-0.10.0/onlineforecast/inst/doc/setup-and-use-model.html | 1018 ++-------- onlineforecast-0.10.0/onlineforecast/inst/doc/setup-data.R | 37 onlineforecast-0.10.0/onlineforecast/inst/doc/setup-data.Rmd | 44 onlineforecast-0.10.0/onlineforecast/inst/doc/setup-data.html | 88 onlineforecast-0.10.0/onlineforecast/man/as.data.list.Rd | 30 onlineforecast-0.10.0/onlineforecast/man/cache_name.Rd | 9 onlineforecast-0.10.0/onlineforecast/man/complete_cases.Rd |only onlineforecast-0.10.0/onlineforecast/man/depth.Rd |only onlineforecast-0.10.0/onlineforecast/man/flattenlist.Rd |only onlineforecast-0.10.0/onlineforecast/man/forecastmodel.Rd | 4 onlineforecast-0.10.0/onlineforecast/man/in_range.Rd | 4 onlineforecast-0.10.0/onlineforecast/man/lagdf.Rd | 4 onlineforecast-0.10.0/onlineforecast/man/lagdl.Rd |only onlineforecast-0.10.0/onlineforecast/man/lapply_cbind.Rd | 4 onlineforecast-0.10.0/onlineforecast/man/lapply_cbind_df.Rd | 4 onlineforecast-0.10.0/onlineforecast/man/lapply_rbind.Rd | 4 onlineforecast-0.10.0/onlineforecast/man/lapply_rbind_df.Rd | 4 onlineforecast-0.10.0/onlineforecast/man/lm_fit.Rd | 13 onlineforecast-0.10.0/onlineforecast/man/lm_optim.Rd | 6 onlineforecast-0.10.0/onlineforecast/man/make_periodic.Rd |only onlineforecast-0.10.0/onlineforecast/man/make_tday.Rd | 23 onlineforecast-0.10.0/onlineforecast/man/plot_ts.Rd | 8 onlineforecast-0.10.0/onlineforecast/man/residuals.Rd | 9 onlineforecast-0.10.0/onlineforecast/man/rls_fit.Rd | 2 onlineforecast-0.10.0/onlineforecast/man/rls_optim.Rd | 10 onlineforecast-0.10.0/onlineforecast/man/rls_summary.Rd | 11 onlineforecast-0.10.0/onlineforecast/man/rmse.Rd | 2 onlineforecast-0.10.0/onlineforecast/man/score.Rd | 30 onlineforecast-0.10.0/onlineforecast/man/step_optim.Rd |only onlineforecast-0.10.0/onlineforecast/vignettes/forecast-evaluation.Rmd | 217 +- onlineforecast-0.10.0/onlineforecast/vignettes/model-selection.Rmd |only onlineforecast-0.10.0/onlineforecast/vignettes/setup-and-use-model.Rmd | 62 onlineforecast-0.10.0/onlineforecast/vignettes/setup-data.Rmd | 44 onlineforecast-0.9.3/onlineforecast/R/rls_reduce.R |only onlineforecast-0.9.3/onlineforecast/R/score_fit.R |only onlineforecast-0.9.3/onlineforecast/man/as.data.list.data.frame.Rd |only onlineforecast-0.9.3/onlineforecast/man/score_fit.Rd |only 78 files changed, 1674 insertions(+), 1764 deletions(-)
More information about onlineforecast at CRAN
Permanent link
Title: Hacks for 'ggplot2'
Description: A 'ggplot2' extension that does a variety of little
helpful things. The package extends 'ggplot2' facets through
customisation, by setting individual scales per panel, resizing panels
and providing nested facets. Also allows multiple colour and fill
scales per plot. Also hosts a smaller collection of stats, geoms and axis
guides.
Author: Teun van den Brand [aut, cre] (<https://orcid.org/0000-0002-9335-7468>)
Maintainer: Teun van den Brand <tahvdbrand@gmail.com>
Diff between ggh4x versions 0.1.2.1 dated 2021-02-11 and 0.2.0 dated 2021-08-21
DESCRIPTION | 23 LICENSE | 4 MD5 | 202 +++--- NAMESPACE | 213 +++--- NEWS.md | 161 +++-- R/conveniences.R |only R/facet_grid2.R |only R/facet_manual.R |only R/facet_nested.R | 788 +++++++++---------------- R/facet_nested_wrap.R | 432 +++---------- R/facet_wrap2.R | 861 +++++++++++++-------------- R/facetted_pos_scales.R | 670 +++++++++++---------- R/force_panelsize.R | 250 ++++---- R/geom_pointpath.R | 674 ++++++++++----------- R/geom_rectrug.R | 10 R/geom_text_aimed.R | 394 ++++++------ R/ggh4x-package.R | 37 - R/guide_axis_logticks.R | 396 ++++++------ R/guide_axis_manual.R |only R/guide_axis_minor.R | 402 ++++++------ R/guide_axis_nested.R | 514 ++++++++-------- R/guide_axis_truncated.R | 538 +++++++++-------- R/guide_axis_utils.R | 331 +++++----- R/guide_dendrogram.R | 419 ++++++------- R/guide_stringlegend.R | 710 +++++++++++----------- R/help_secondary.R |only R/position_disjoint_ranges.R | 256 ++++---- R/position_lineartrans.R | 304 ++++----- R/scale_dendrogram.R | 286 ++++----- R/stat_difference.R |only R/stat_funxy.R | 277 ++++---- R/stat_rle.R | 402 ++++++------ R/stat_roll.R | 442 +++++++------- R/strip_nested.R |only R/strip_themed.R |only R/strip_vanilla.R |only R/utils.R | 365 ++--------- R/utils_grid.R |only R/utils_gtable.R |only README.md | 359 +++++------ build/vignette.rds |binary inst/doc/Facets.R | 351 ++++++++--- inst/doc/Facets.Rmd | 576 +++++++++++++----- inst/doc/Facets.html | 750 +++++++++++++++--------- inst/doc/Miscellaneous.R | 270 ++++---- inst/doc/Miscellaneous.Rmd | 386 ++++++------ inst/doc/Miscellaneous.html | 610 +++++++++---------- inst/doc/PositionGuides.R | 386 +++++++----- inst/doc/PositionGuides.Rmd | 588 +++++++++++------- inst/doc/PositionGuides.html | 729 +++++++++++++---------- inst/doc/Statistics.R | 502 ++++++++-------- inst/doc/Statistics.Rmd | 770 +++++++++++++----------- inst/doc/Statistics.html | 904 +++++++++++++++-------------- inst/doc/ggh4x.R | 94 +-- inst/doc/ggh4x.Rmd | 136 ++-- inst/doc/ggh4x.html | 414 ++++++------- man/center_limits.Rd | 2 man/distribute_args.Rd |only man/facet_grid2.Rd |only man/facet_manual.Rd |only man/facet_nested.Rd | 374 ++++++----- man/facet_nested_wrap.Rd | 314 +++++----- man/facet_wrap2.Rd | 241 ++++--- man/facetted_pos_scales.Rd | 172 ++--- man/figures/README-facets-1.png |binary man/figures/README-multicolour-1.png |binary man/force_panelsizes.Rd | 116 +-- man/geom_pointpath.Rd | 6 man/geom_rectmargin.Rd | 10 man/geom_text_aimed.Rd | 295 ++++----- man/ggh4x-package.Rd | 60 - man/ggh4x_extensions.Rd | 80 +- man/ggsubset.Rd | 2 man/guide_axis_logticks.Rd | 239 ++++--- man/guide_axis_manual.Rd |only man/guide_axis_minor.Rd | 201 +++--- man/guide_axis_nested.Rd | 249 ++++--- man/guide_axis_truncated.Rd | 224 ++++--- man/guide_dendro.Rd | 210 +++--- man/guide_stringlegend.Rd | 224 +++---- man/help_secondary.Rd |only man/position_disjoint_ranges.Rd | 4 man/position_lineartrans.Rd | 4 man/scale_dendrogram.Rd | 234 +++---- man/stat_difference.Rd |only man/stat_funxy.Rd | 2 man/stat_rle.Rd | 282 ++++----- man/strip_nested.Rd |only man/strip_themed.Rd |only man/strip_vanilla.Rd |only man/weave_factors.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-conveniences.R |only tests/testthat/test-facet_grid2.R |only tests/testthat/test-facet_manual.R |only tests/testthat/test-facet_nested.R | 671 ++++++++++----------- tests/testthat/test-facet_nested_wrap.R | 181 ++--- tests/testthat/test-facet_wrap2.R | 180 ++--- tests/testthat/test-facetted_pos_scales.R | 751 ++++++++++++------------ tests/testthat/test-geom_text_aimed.R | 56 - tests/testthat/test-guide_axis_logticks.R | 208 +++--- tests/testthat/test-guide_axis_manual.R |only tests/testthat/test-guide_axis_minor.R | 180 ++--- tests/testthat/test-guide_axis_truncated.R | 190 +++--- tests/testthat/test-guide_stringlegend.R | 80 +- tests/testthat/test-help_secondary.R |only tests/testthat/test-scale_dendrogram.R | 338 +++++----- tests/testthat/test-stat_difference.R |only tests/testthat/test-strips.R |only tests/testthat/test-utils.R | 113 +-- vignettes/Facets.Rmd | 576 +++++++++++++----- vignettes/Facets.md |only vignettes/Miscellaneous.Rmd | 386 ++++++------ vignettes/PositionGuides.Rmd | 588 +++++++++++------- vignettes/Statistics.Rmd | 770 +++++++++++++----------- vignettes/ggh4x.Rmd | 136 ++-- 116 files changed, 14319 insertions(+), 12818 deletions(-)
Title: Translate Integers into English
Description: Allow numbers to be presented in an English language
version, one, two, three, ... Ordinals are also available,
first, second, third, ... and indefinite article choice, "a" or "an".
Author: John Fox, Bill Venables, Anthony Damico and Anne Pier Salverda
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between english versions 1.2-5 dated 2020-01-26 and 1.2-6 dated 2021-08-21
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/ordinal.R | 9 +++++---- build/vignette.rds |binary inst/doc/the-english-patient.pdf |binary 5 files changed, 14 insertions(+), 13 deletions(-)
Title: Variance-Covariance Matrix for Multivariate Meta-Analysis
Description: Compute variance-covariance matrix for multivariate meta-analysis. Effect sizes include correlation (r), mean difference (MD), standardized mean difference (SMD), log odds ratio (logOR), log risk ratio (logRR), and risk difference (RD).
Author: Min Lu <m.lu6@umiami.edu>
Maintainer: Min Lu <m.lu6@umiami.edu>
Diff between metavcov versions 1.1 dated 2017-03-29 and 2.1 dated 2021-08-21
DESCRIPTION | 11 - MD5 | 53 +++---- R/lgOR.vcov.R | 46 +++--- R/lgRR.vcov.R | 46 +++--- R/md.vcov.R | 39 ++--- R/mix.vcov.R | 326 ++++++++++++++++++++++++------------------------ R/r.vcov.R | 298 +++++++++++++++++++++---------------------- R/rd.vcov.R | 46 +++--- R/smd.vcov.R | 54 +++---- inst |only man/lgOR.vcov.Rd | 30 ++-- man/lgRR.vcov.Rd | 28 ++-- man/lgor_lgrr.Rd | 28 ++-- man/lgor_rd.Rd | 24 +-- man/lgrr_rd.Rd | 24 +-- man/md.vcov.Rd | 24 +-- man/md_lgor.Rd | 18 +- man/md_lgrr.Rd | 18 +- man/md_rd.Rd | 18 +- man/md_smd.Rd | 18 +- man/metavcov-package.Rd | 14 +- man/mix.vcov.Rd | 50 +++---- man/r.vcov.Rd | 26 +-- man/rd.vcov.Rd | 28 ++-- man/smd.vcov.Rd | 22 +-- man/smd_lgor.Rd | 18 +- man/smd_lgrr.Rd | 18 +- man/smd_rd.Rd | 18 +- 28 files changed, 673 insertions(+), 670 deletions(-)
Title: Tabulate Descriptive Statistics in Multiple Formats
Description: Creates a table of descriptive statistics
for factor and numeric columns in a data frame. Displays
these by groups, if any. Highly customizable, with support
for 'html' and 'pdf' provided by 'kableExtra'. Respects
original column order, column labels, and factor level order.
See ?tablet.data.frame and vignettes.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between tablet versions 0.3.2 dated 2021-07-18 and 0.4.0 dated 2021-08-21
tablet-0.3.2/tablet/inst/shiny-examples/mesa/target.R |only tablet-0.4.0/tablet/DESCRIPTION | 8 tablet-0.4.0/tablet/MD5 | 32 tablet-0.4.0/tablet/NAMESPACE | 2 tablet-0.4.0/tablet/R/mesa.R | 2 tablet-0.4.0/tablet/R/tablet.R | 2 tablet-0.4.0/tablet/R/xtable.R |only tablet-0.4.0/tablet/inst/doc/tablet-introduction-html.html | 4 tablet-0.4.0/tablet/inst/doc/tablet-introduction-pdf.R | 11 tablet-0.4.0/tablet/inst/doc/tablet-introduction-pdf.Rmd | 18 tablet-0.4.0/tablet/inst/doc/tablet-introduction-pdf.pdf |binary tablet-0.4.0/tablet/inst/shiny-examples/mesa/app.R | 563 +++++----- tablet-0.4.0/tablet/inst/shiny-examples/mesa/data/adsl.sas7bdat |only tablet-0.4.0/tablet/inst/shiny-examples/mesa/data/adsl.yaml |only tablet-0.4.0/tablet/inst/shiny-examples/mesa/data/mtcars.conf | 23 tablet-0.4.0/tablet/man/as_xtable.Rd |only tablet-0.4.0/tablet/man/as_xtable.tablet.Rd |only tablet-0.4.0/tablet/man/mesa.Rd | 2 tablet-0.4.0/tablet/man/tablet.data.frame.Rd | 2 tablet-0.4.0/tablet/vignettes/tablet-introduction-pdf.Rmd | 18 20 files changed, 407 insertions(+), 280 deletions(-)
Title: Exact Sequential Analysis for Poisson and Binomial Data
Description: Functions to calculate exact critical values, statistical power, expected time to signal, and required sample sizes for performing exact sequential analysis. All these calculations can be done for either Poisson or binomial data, for continuous or group sequential analyses, and for different types of rejection boundaries. In case of group sequential analyses, the group sizes do not have to be specified in advance and the alpha spending can be arbitrarily settled.
Author: Ivair Ramos Silva and Martin Kulldorff
Maintainer: Ivair Ramos Silva <jamesivair@yahoo.com.br>
Diff between Sequential versions 3.3.2 dated 2021-08-18 and 3.3.3 dated 2021-08-21
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/Analyze.Poisson.R | 2 +- R/Performance.AlphaSpend.Poisson.R | 4 ++-- R/SampleSize.Poisson.R | 21 ++++++++++++++++++--- man/SampleSize.Poisson.Rd | 2 +- man/Sequential-package.Rd | 8 ++++++-- 7 files changed, 38 insertions(+), 19 deletions(-)
Title: Factorization of Sparse Counts Matrices Through Poisson
Likelihood
Description: Creates a low-rank factorization of a sparse counts matrix by maximizing Poisson likelihood with l1/l2 regularization
with all non-negative latent factors (e.g. for recommender systems or topic modeling) (Cortes, (2018) <arXiv:1811.01908>).
Similar to hierarchical Poisson factorization, but follows an optimization-based approach with regularization instead of a
hierarchical structure, and is fit through gradient-based methods instead of variational inference.
Author: David Cortes [aut, cre, cph],
Jean-Sebastien Roy [cph] (Copyright holder of included tnc library),
Stephen Nash [cph] (Copyright holder of included tnc library)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between poismf versions 0.3.1 dated 2021-07-13 and 0.3.1-1 dated 2021-08-21
DESCRIPTION | 18 ++++++++++++++---- MD5 | 15 ++++++++------- R/poismf.R | 11 +++++++++++ inst |only man/poismf.Rd | 3 +++ src/poismf.c | 10 ++++++++++ src/poismf.h | 1 + src/rwrapper.c | 9 +++++++++ src/tnc.c | 6 ------ 9 files changed, 56 insertions(+), 17 deletions(-)
Title: Nonparametric Probability Density Estimator
Description: Farmer, J., D. Jacobs (2108) <DOI:10.1371/journal.pone.0196937>. A nonparametric density estimator based on the maximum-entropy method. Accurately predicts a probability density function (PDF) for random data using a novel iterative scoring function to determine the best fit without overfitting to the sample.
Author: Jenny Farmer <jfarmer6@uncc.edu> and Donald Jacobs <djacobs1@uncc.ecu>
Maintainer: Jenny Farmer <jfarmer6@uncc.edu>
Diff between PDFEstimator versions 2.2 dated 2021-03-21 and 3.0 dated 2021-08-21
DESCRIPTION | 8 +- MD5 | 34 ++++++----- NAMESPACE | 6 +- R/convertToPDFe.R |only R/estimatePDF.R | 58 ++++++++++++++----- R/print.R |only R/summary.R |only man/convertToPDFe.Rd |only man/estimatePDF.Rd | 12 ++-- src/ChebyShev.h | 2 src/InputData.cpp | 1 src/InputData.h | 2 src/InputParameters.cpp | 13 +++- src/InputParameters.h | 5 + src/MinimizeScore.cpp | 8 +- src/PDFMain.cpp | 18 ++---- src/WriteResults.cpp | 142 +++++++++++++++++++++++++++++------------------- src/WriteResults.h | 1 src/callPDF.cpp | 12 +++- src/callPDF.h | 3 - 20 files changed, 209 insertions(+), 116 deletions(-)
Title: Find Related Items and Lexical Dimensions in a Lexicon
Description: Implements code to identify lexical competitors in a given list
of words. We include many of the standard competitor types used in spoken word
recognition research, such as functions to find cohorts, neighbors, and
rhymes, amongst many others. The package includes documentation for using a
variety of lexicon files, including those with form codes made up of multiple
letters (i.e., phoneme codes) and also basic orthographies. Importantly, the
code makes use of multiple CPU cores and vectorization when possible, making
it extremely fast and able to handle large lexicons. Additionally, the package
contains documentation for users to easily write new functions, allowing
researchers to examine other relationships within a lexicon. <https://psyarxiv.com/8dyru/>.
Author: ZhaoBin Li [aut, cre],
Anne Marie Crinnion [aut],
James S. Magnuson [aut, cph]
Maintainer: ZhaoBin Li <bzilplj@gmail.com>
Diff between LexFindR versions 1.0.0 dated 2021-08-09 and 1.0.1 dated 2021-08-21
LexFindR-1.0.0/LexFindR/vignettes/my-vignette_cache/html/parallelize_90be3ae3a970033fe014bff7cfd4db9b.RData |only LexFindR-1.0.0/LexFindR/vignettes/my-vignette_cache/html/parallelize_90be3ae3a970033fe014bff7cfd4db9b.rdb |only LexFindR-1.0.0/LexFindR/vignettes/my-vignette_cache/html/parallelize_90be3ae3a970033fe014bff7cfd4db9b.rdx |only LexFindR-1.0.1/LexFindR/DESCRIPTION | 13 +---- LexFindR-1.0.1/LexFindR/MD5 | 14 ++--- LexFindR-1.0.1/LexFindR/NEWS.md | 4 + LexFindR-1.0.1/LexFindR/README.md | 8 --- LexFindR-1.0.1/LexFindR/inst/doc/my-vignette.html | 26 +++++----- LexFindR-1.0.1/LexFindR/vignettes/my-vignette_cache/html/parallelize_f8b10b8b3be82e281b148b3e2a0f322a.RData |only LexFindR-1.0.1/LexFindR/vignettes/my-vignette_cache/html/parallelize_f8b10b8b3be82e281b148b3e2a0f322a.rdb |only LexFindR-1.0.1/LexFindR/vignettes/my-vignette_cache/html/parallelize_f8b10b8b3be82e281b148b3e2a0f322a.rdx |only 11 files changed, 30 insertions(+), 35 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Author: Tomasz Kalinowski [ctb, cph, cre],
Daniel Falbel [ctb, cph],
JJ Allaire [aut, cph],
François Chollet [aut, cph],
RStudio [ctb, cph, fnd],
Google [ctb, cph, fnd],
Yuan Tang [ctb, cph] (<https://orcid.org/0000-0001-5243-233X>),
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigrid Keydana [ctb]
Maintainer: Tomasz Kalinowski <tomasz.kalinowski@rstudio.com>
Diff between keras versions 2.4.0 dated 2021-03-29 and 2.6.0 dated 2021-08-21
keras-2.4.0/keras/man/loss_binary_crossentropy.Rd |only keras-2.4.0/keras/man/loss_mean_squared_error.Rd |only keras-2.6.0/keras/DESCRIPTION | 19 keras-2.6.0/keras/MD5 | 356 +- keras-2.6.0/keras/NAMESPACE | 88 keras-2.6.0/keras/NEWS.md | 191 + keras-2.6.0/keras/R/Layer.R | 128 keras-2.6.0/keras/R/activations.R | 56 keras-2.6.0/keras/R/applications.R | 333 +- keras-2.6.0/keras/R/backend.R | 1055 +++--- keras-2.6.0/keras/R/callbacks.R | 434 +- keras-2.6.0/keras/R/constraints.R | 63 keras-2.6.0/keras/R/datasets.R | 99 keras-2.6.0/keras/R/freeze.R | 29 keras-2.6.0/keras/R/generics.R |only keras-2.6.0/keras/R/history.R | 108 keras-2.6.0/keras/R/initializers.R | 143 keras-2.6.0/keras/R/install.R | 256 - keras-2.6.0/keras/R/layer-attention.R | 81 keras-2.6.0/keras/R/layer-custom.R | 172 + keras-2.6.0/keras/R/layer-methods.R | 90 keras-2.6.0/keras/R/layer-text_vectorization.R | 128 keras-2.6.0/keras/R/layer-wrappers.R | 37 keras-2.6.0/keras/R/layers-activations.R | 92 keras-2.6.0/keras/R/layers-convolutional.R | 641 ++-- keras-2.6.0/keras/R/layers-core.R | 335 +- keras-2.6.0/keras/R/layers-dropout.R | 97 keras-2.6.0/keras/R/layers-embedding.R | 42 keras-2.6.0/keras/R/layers-features.R | 30 keras-2.6.0/keras/R/layers-locally-connected.R | 100 keras-2.6.0/keras/R/layers-merge.R | 112 keras-2.6.0/keras/R/layers-noise.R | 54 keras-2.6.0/keras/R/layers-normalization.R | 66 keras-2.6.0/keras/R/layers-pooling.R | 257 - keras-2.6.0/keras/R/layers-recurrent.R | 221 - keras-2.6.0/keras/R/losses.R | 455 ++- keras-2.6.0/keras/R/metrics-callback.R | 129 keras-2.6.0/keras/R/metrics.R | 1512 +++++++++- keras-2.6.0/keras/R/model-custom.R | 24 keras-2.6.0/keras/R/model-legacy.R | 58 keras-2.6.0/keras/R/model-persistence.R | 322 +- keras-2.6.0/keras/R/model.R | 819 +++-- keras-2.6.0/keras/R/optimizers.R | 139 keras-2.6.0/keras/R/package.R | 116 keras-2.6.0/keras/R/preprocessing.R | 487 +-- keras-2.6.0/keras/R/py-classes.R |only keras-2.6.0/keras/R/reexports.R | 3 keras-2.6.0/keras/R/regularizers.R | 10 keras-2.6.0/keras/R/seed.R | 1 keras-2.6.0/keras/R/timeseries.R | 8 keras-2.6.0/keras/R/utils.R | 185 - keras-2.6.0/keras/R/wrapper_custom.R | 64 keras-2.6.0/keras/build/vignette.rds |binary keras-2.6.0/keras/inst/doc/applications.html | 400 -- keras-2.6.0/keras/inst/doc/custom_layers.html | 652 +--- keras-2.6.0/keras/inst/doc/custom_models.html | 320 -- keras-2.6.0/keras/inst/doc/faq.html | 632 +--- keras-2.6.0/keras/inst/doc/functional_api.html | 684 +--- keras-2.6.0/keras/inst/doc/guide_keras.html | 652 +--- keras-2.6.0/keras/inst/doc/index.html | 300 - 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Title: Access EPA 'ECHO' Data
Description: An R interface to United States Environmental
Protection Agency (EPA) Environmental Compliance
History Online ('ECHO') Application Program Interface
(API). 'ECHO' provides information about EPA permitted
facilities, discharges, and other reporting info
associated with permitted entities. Data are obtained
from <https://echo.epa.gov/>.
Author: Michael Schramm [aut, cre, cph]
Maintainer: Michael Schramm <michael.schramm@ag.tamu.edu>
Diff between echor versions 0.1.5 dated 2020-08-05 and 0.1.6 dated 2021-08-21
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